Api15

This is a description of the 2015 api to docking.org services.

Background

Docking remains too difficult for many people, even experts. One of the reasons is that it requires a complex software and hardware environment that requires much effort and ongoing maintenance. The purpose of this API is to make important steps in the docking process more accessible. The major application areas are:

• docking - non covalent docking
• covalent - covalent docking
• zinc - database preparation and processing, including covalent docking libraries
• dude - decoys as sanity checks, when actives are available

This API aims to allow all simple transactions to be run under program control on our servers. The user may then elect to download the materials (docking prep files, databases) for local fine tuning on the user's machines, or to continue the calculation with less control on our servers.

Syntax

The URL takes one of two forms

1. api.docking.org/vX/application/action/arguments

1. api.docking.org/vX/job_number/application/subaction/arguments

Where application is one of: docking, covalent, zinc, decoys. We take up the arguments of each of these below:

Applications

application:docking

Supported actions are: pdb, upload, listpdb, jobs, myjobs

pdb: specify pdb code for automatic (be_blasti) docking

upload: specify receptor and binding site. if binding site not specified, pockets are picked.

list: list all pdb codes supported

jobs: list all recent jobs in system

myjobs: list my recent jobs (based on apikey)

Sub-actions for operating on a docking job

info : display what kind of job it is, when submitted, current status. pickpockets : pick pockets library: specify library for docking

application:covalent

supported actions are: upload, jobs, myjobs

upload: specify receptor and covalent attachment point.

Sub-actions for operating on a covalent docking job

info: display what kind of job it is, when submitted, current status library: specify library for docking

application: decoys

Supported actions are: make, get, list

make: make decoys based on uploaded molecules

get: specify gene, get both actives and decoys from chembl for that gene

list: list all genes for which decoys (and actives) are available.

Subactions for acting on a decoys job

Supported subactions are: download

application: zinc

supported actions: upload, download, prepare, subset, hotsubset

upload: upload molecules for standard preparation using zinc pipeline. Libraries uploaded in this way may be used by docking

download: download large custom subset in any format.

prepare: make sure 3D versions of a subset are ready for download (this may take weeks)

subset: create a subset for docking,

hotsubset: prepare covalent docking database

Sub-actions for application: zinc

Supported subactions are: download

Use Case examples

Create a database of in stock commercially available arylsulfonamides for docking =

api.docking.org/v1/zinc/subset/substances/smiles,sub_id/substance contains c1ccccc1S(=O)(=O)N&catalog.purchasable gt 20

This is created as job # 122334

Now find a upload a structure and docking this library to it

api.docking.org/v1/dock/upload/rec=rec.pdb,lig=xtal-lig.pdb,lib=122334

This is created as job # 556677

Download the docking results for docking on the client

api.docking.org/v1/556677/download/all

Download the arylsulfonamide database created above in db2 format

api.docking.org/v1/122334/download/db2

Upload a structure of unknown function and unknown binding site, identify binding site

api.docking.org/v1/dock/upload/rec=rec.pdb  # implies pocket picking since no binding site specified

Uploads as dock jobs 32234

Download the pockets picked above together with basic cleanup and normalization of the structure

api.docking.org/v1/dock/32234/download/all

Upload a structure and a binding site specification, but still request that pockets be picked:

api.docking.org/v1/dock/upload/rec=rec.pdb&lig=xtal-lig.pdb&pick=true

Covalent docking. Upload a structure, and scan for eligible covalent attachment points.

api.docking.org/v1/covalent/rec=rec.pdb

covalent docking. Upload a structure and a covalent attachment point.

api.docking.org/v1/covalent/rec=rec.pdb&site=Asp A 234

Covalent docking. Prepare library for covalent docking.

api.docking.org/v1/covalent/library/list1/list2/reactionsmarts

where list1 and list2 is a previously created subset using the zinc api and reaction smarts is a chemical reaction to combine molecule from list1 with molecules from list2 to create a new combinatorial library.

covalent docking. prepare hot covalent docking library.